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Genome Biol. 2016 Nov 25;17(1):238.

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.

Author information

1
Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway. ola.brynildsrud@fhi.no.
2
Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.
3
Hanze University of Applied Sciences, Groningen, The Netherlands.

Abstract

Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .

KEYWORDS:

Accessory genome; Annotation; Association; Bacteria; Genome-wide association studies (GWAS); Genomics; Next-generation sequencing (NGS); Pan-genome; Prokaryote; Python; Whole-genome sequencing (WGS)

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